Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Yuan, Chao ^a   Wang, Xiaolong ^a   Geng, Rongqing ^a,b   He, Xiaolin ^a   Qu, Lei ^c   Chen, Yulin ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b YANCHENG TEACHERS UNIVERSITY   (China)

^c YULIN UNIVERSITY   (China)

Author keywords

Cashmere goat; Hair cycle; Hair follicle; MicroRNAs; Skin; Solexa sequencing

Indexed keywords

MICRORNA;

ANIMAL TISSUE; ARTICLE; BIOLOGICAL ACTIVITY; BREEDING; CAPRA HIRCUS; CATAGEN; CONTROLLED STUDY; DEVELOPMENTAL STAGE; ENDOCYTOSIS; FOCAL ADHESION; GENE EXPRESSION PROFILING; GENE LOCATION; GENE TARGETING; GOAT; HAIR FOLLICLE; HAIR GROWTH; NONHUMAN; POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SIGNAL TRANSDUCTION; TELOGEN;

ANIMALS; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GOATS; HAIR FOLLICLE; MICRORNAS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, RNA; SKIN;

CAPRA HIRCUS; MUS;

EID: 84880867107     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-511     Document Type: Article

References (44)

1. Krause K, Foitzik K. Biology of the Hair Follicle: The Basics. Semin Cutan Med Surg 2006, 25:2-10. 10.1016/j.sder.2006.01.002, 16616298.
2. Stenn KS, Paus R. Controls of Hair Follicle Cycling. Physiol Rev 2001, 81:449-494.
3. Schmidt Ullrich R, Paus R. Molecular principles of hair follicle induction and morphogenesis. BioEssays 2005, 27:247-261. 10.1002/bies.20184, 15714560.
4. Fuchs E. Scratching the surface of skin development. Nature 2007, 445:834-842. 10.1038/nature05659, 2405926, 17314969.
5. Mikkola ML. Genetic basis of skin appendage development. Semin Cell Dev Biol 2007, 18:225-236. 10.1016/j.semcdb.2007.01.007, 17317239.
6. Schneider MR, Schmidt Ullrich R, Paus R. The Hair Follicle as a Dynamic Miniorgan. Curr Biol 2009, 19:R132-R142. 10.1016/j.cub.2008.12.005, 19211055.
7. Paus R, Foitzik K. In search of the " hair cycle clock" : a guided tour. Differentiation 2004, 72:489-511. 10.1111/j.1432-0436.2004.07209004.x, 15617561.
8. Schneider MR. MicroRNAs as novel players in skin development, homeostasis and disease. British Association of Dermatologists 2012, 166:22-28.
9. Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development 2005, 132:4653-4662. 10.1242/dev.02073, 16224045.
10. Yi R, Poy MN, Stoffel M, Fuchs E. A skin microRNA promotes differentiation by repressing 'stemness'. Nature 2008, 452:225-229. 10.1038/nature06642, 18311128.
11. Yi R, O'Carroll D, Pasolli HA, Zhang Z, Dietrich FS, Tarakhovsky A, Fuchs E. Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs. Nat Genet 2006, 38:356-362. 10.1038/ng1744, 16462742.
12. Lena AM, Shalom-Feuerstein R, Rivetti di Val Cervo P, Aberdam D, Knight RA, Melino G, Candi E. miR-203 represses 'stemness' by repressing DeltaNp63. Cell Death Differ 2008, 15:1187-1195. 10.1038/cdd.2008.69, 18483491.
13. McKenna DJ, McDade SS, Patel D, McCance DJ. MiR-203 expression in keratinocytes is dependent on regulation of p53 levels by E6. J Virol 2010, 84:10644-10652. 10.1128/JVI.00703-10, 2950558, 20702634.
14. Andl T, Murchison EP, Liu F, Zhang Y, Yunta-Gonzalez M, Tobias JW, Andl CD, Seykora JT, Hannon GJ, Millar SE. The miRNA-processing enzyme dicer is essential for the morphogenesis and maintenance of hair follicles. Curr Biol 2006, 16:1041-1049. 10.1016/j.cub.2006.04.005, 2996092, 16682203.
15. Mardaryev AN, Ahmed MI, Vlahov NV, Fessing MY, Gill JH, Sharov AA, Botchkareva NV. Micro-RNA-31 controls hair cycle-associated changes in gene expression programs of the skin and hair follicle. FASEB J 2010, 24:3869-3881. 10.1096/fj.10-160663, 20522784.
16. Hai-yan XI, Huan-min Z, Yan Z. Construction and Analysis of Subtractive cDNA Library of Secondary Follicle in Anagen in cashmere goat. Scientia Agricultura Sinica 2009, 42:3749-3754.
17. Su R, Zhang WG, Sharma R, Chang ZL, Yin J, Li JQ. Characterization of BMP2 gene expression in embryonic and adult Inner Mongolia cashmere goat (Capra hircus) hair follicles. Can J Anim Sci 2009, 89:457-462.
18. Wenguang Z, Jianghong W, Jinquan L, Yashizawa M. A Subset of Skin-Expressed microRNAs with Possible Roles in Goat and Sheep Hair Growth Based on Expression Profiling of Mammalian microRNAs. OMICS 2007, 11:385-396. 10.1089/omi.2006.0031, 18092910.
19. Hao D-C, Yang L, Xiao P-G, Liu M. Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis. Physiol Plant 2012, 146:388-403. 10.1111/j.1399-3054.2012.01668.x, 22708792.
20. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
21. Wu L, Fan J, Belasco JG. microRNAs direct rapid dead-enylation of mRNA. Proc Natl Acad Sci 2006, 103:4034-4039. 10.1073/pnas.0510928103, 1449641, 16495412.
22. Easow G, Teleman AA, Cohen SM. Isolation of microRNA targets by miRNP immunopurification. RNA 2007, 13:1198-1204. 10.1261/rna.563707, 1924889, 17592038.
23. Huang J, Ju Z, Li Q, Hou Q, Wang C, Li J, Li R, Wang L, Sun T, Hang S, Gao Y, Hou M, Zhong J. Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci 7:1016-1026.
24. Chen X, Li Q, Wang J, Guo X, Jiang X, Ren Z, Weng G, Sun G, Wang X, Liu Y, Ma L, Chen JY, Wang J, Zen K, Zhang J, Zhang CY. Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 2009, 10:R78. 10.1186/gb-2009-10-7-r78, 2728532, 19615057.
25. Ji Z, Wang G, Xie Z, Zhang C, Wang J. Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa Solexa-sequencing technology. Mol Biol Rep 2012, 39:9361-9371. 10.1007/s11033-012-1779-5, 22763736.
26. Liu Z, Xiao H, Li H, Zhao Y, Lai S, Yu X, Cai T, Du C, Zhang W, Li J. Identification of conserved and novel microRNAs in cashmere goat skin by deep sequencing. PLoS One 2012, 7(12):e50001. 10.1371/journal.pone.0050001, 3517574, 23236360.
27. Li G, Li Y, Li X, Ning X, Li M, Yang G. MicroRNA identity and abundance in developing swine adipose tissue as determined by Solexa sequencing. J Cell Biochem 2011, 112:1318-1328. 10.1002/jcb.23045, 21312241.
28. Li T, Wu R, Zhang Y, Zhu D. A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs. BMC Genomics 2011, 12:186. 10.1186/1471-2164-12-186, 3107184, 21486491.
29. Stefani G, Slack FJ. Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 2008, 9:219-230. 10.1038/nrm2347, 18270516.
30. Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L. Novel microRNAs uncovered by Solexa sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.). Beauv. Funct Integr Genomics 2009, 9:499-511. 10.1007/s10142-009-0128-9, 19499258.
31. Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA. let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. J Biol Chem 2009, 284:6605-6609. 2652271, 19126550.
32. Shatseva T, Lee DY, Deng Z, Yang BB. MicroRNA miR-199a-3p regulates cell proliferation and survival by targeting caveolin-2. J Cell Sci 2011, 124:2826-2836. 10.1242/jcs.077529, 21807947.
33. Sun J-Y, Huang Y, Li J-P, Zhang X, Wang L, Meng Y-L, Yan B, Bian Y-Q, Zhao J, Wang W-Z, Yang A-G, Zhang R. MicroRNA-320a suppresses human colon cancer cell proliferation by directly targeting β-catenin. Biochem Biophys Res Commun 2012, 420:787-792. 10.1016/j.bbrc.2012.03.075, 22459450.
34. Wulczyn FG, Smirnova L, Rybak A, Brandt C, Kwidzinski E, Ninnemann O, Strehle M, Seiler A, Schumacher S, Nitsch R. Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J 2007, 21:415-426. 10.1096/fj.06-6130com, 17167072.
35. Thum T, Catalucci D, Bauersachs J. MicroRNAs: novel regulators in cardiac development and disease. Cardiovasc Res 2008, 79:562-570. 10.1093/cvr/cvn137, 18511432.
36. Harris KS, Zhang Z, McManus MT, Harfe BD, Sun X. Dicer function is essential for lung epithelium morphogenesis. Proc Natl Acad Sci USA 2006, 103:2208-2213. 10.1073/pnas.0510839103, 1413733, 16452165.
37. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN, Lee T-H, Miano JM, Ivey KN, Srivastava D. miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 2009, 460:705-710. 2769203, 19578358.
38. Chen J-F, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon1 FL, Wang DZ. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2005, 38:228-233. 2538576, 16380711.
39. Millara SE, Willerta K, Salinasa PC, Roelinka H, Nussea R, Sussmanc DJ, Barsha GS. WNTS ignaling in the Control of Hair Growth and Structure. Dev Biol 1999, 207:133-149. 10.1006/dbio.1998.9140, 10049570.
40. Foitzik K, Paus R, Doetschman T, Dotto GP. The TGF-beta2 isoform is both a required and sufficient inducer of murine hair follicle morphogenesis. Dev Biol 1999, 212:278-289. 10.1006/dbio.1999.9325, 10433821.
41. Headon DJ, Overbeek PA. Involvement of a novel Tnf receptor homologue in hair follicle induction. Nat Genet 1999, 22:370-374. 10.1038/11943, 10431242.
42. Boras K, Hamel PA. Alx4 binding to LEF-1 regulates N-CAM promoter activity. J Biol Chem 2002, 277:1120-1127. 10.1074/jbc.M109912200, 11696550.
43. Assa-Kunik E, Torres IL, Schejter ED, Johnston DS, Shilo BZ. Drosophila follicle cells are patterned by multiple levels of Notch signaling and antagonism between the Notch and JAK/STAT pathways. Development 2007, 134:1161-1169. 10.1242/dev.02800, 17332535.
44. Caifu C, Dana AR, Adam JB, Zhaohui Z, Danny HL, Julie TN, Maura B, Nan LX, Vikram RM, Mark RA, Kai QL, Kenneth JL, Karl JG. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33:e179. 10.1093/nar/gni178, 1292995, 16314309.